Operation SHADOWSTEP
by BlackChaos105
Summary: Two years after the Manhattan Outbreak, Alex Mercer has tracked down and consumed all personnel with knowledge of Hope Idaho, and more importantly, PARIAH. Now, GENTEK has begun a project to take down Mercer once and for all, fighting fire with fire...


**Prototype**

**Operation SHADOWSTEP**

**By BlackChaos105**

**A/N: Before you all start freaking out on me about Uchiha Avenger, let me just say this is the first time I have logged onto Fanfiction in several months, I have been very busy these last few months, and now that school's over, I have some time to myself again, but it won't last long. Senior year's gonna be harder than ever, and my schedule's gonna be jam-packed, so I won't get much time to update any of my work. I'll do what I can, and Uchiha Avenger is next on my priority list. I pre-ordered Prototype and beat it recently, and after finishing the Web of Intrigue subplot, I knew I had to make this, they just left the door too far open to leave it be. Fair warning, most of this story will be told in first person perspective. I will use fonts to code which person's perspective we have jumped to, although from the dialogue you should be able to guess. Well, I hope you all enjoy, and please, NO HATEMAIL ABOUT MY LACK OF UPDATES!**

**BlackChaos, out.**

**Dialogue Key:**

Alex Mercer

_Third Person Narration_

**OC (Named in chapter)**

**Disclaimer: Prototype belongs to Activision and Radical Entertainment**

**Chapter 1**

**Beneath the Surface**

* * *

_**Manhattan Island**_

_**Central Park**_

_**July 15th, 2011**_

Allan Reese, PhD. Biochemist, military ally, GENTEK researcher.

My final target.

As I crept upon the poor man, completely unaware of his fate, anticipation and excitement raced through me. I had spent the last two years hunting Reese and his associates, anyone with a connection to the BLACKLIGHT virus.

Reese was in Central Park, feeding the birds. I was fifty yards away, standing on the sidewalk. In a place as open as Central Park, I knew I had to get creative if I was to get him without getting the authorities involved. I went through every single strategy I had created in the last two years, trying to find the perfect way to eliminate my target. All of his acquaintances were MIA, he knew that. If I assumed their form, he would know it was me.

This is where the knowledge I had gathered would be useful. All the doctors and scientists I had consumed knew human anatomy perfectly, and because of that, so did I.

I focused on my fingertip, imagining a silent and inconspicuous yet deadly weapon. In seconds, my fingertip had become a serrated dart, with a nearly invisible strand of string-like substance attached to it and the rest of my hand. I moved my hand to my pocket, and pointed at Reese as I started walking into the park, hiding behind trees. I watched as the dart launched into his spinal column, and he slumped back in the bench he sat on. The dart had done its job, he was completely paralyzed. I slowly moved closer, staying out of view as small tendrils began to sprout out of the dart and attach to Reese. The consumption had begun. I finally crept behind a tree directly next to him and launched my hand at his neck. I pulled him behind the tree and tore his Adam's apple out of his throat, and then the tendrils pulled him in. I became Allan Reese, and I watched all of his memories before my eyes, scanning for specific key points I would recognize. Then I found it.

"Mercer's body doesn't house DX-1118 any longer, it's become a completely different strain of Blacklight."

"My question is, how did the virus consume his body so discreetly that not even Blackwatch realized it was the virus, and not Mercer?"

"We need to look into that as well. Maybe the process that created Mercer could be replicated. If you can't kill a virus with a cure, perhaps you can kill it with more of said virus…"

I returned to the world around me, under the guise of Allan Reese. I now knew everything that Manhattan had to offer me about Blacklight.

My name is Alex Mercer. I am a scientist. I am a terrorist. I am a killer. I am Blacklight.

* * *

**_Washington D.C_**

**_White House Press Conference_**

**_August 27th, 2011_**

_"Mr. President! What can you tell us about the investigation being done into the Manhattan viral attack? The investigation is been ongoing for the last two years, surely you've uncovered something."_

_"The investigation has been very difficult, as very little has been uncovered from our questioning in the last two years. What remains constant is our prime suspect, Dr. Alexander Mercer, still remains at large. If anyone has any information as to the whereabouts of Dr. Mercer, please contact your local authorities, and they will contact us. Thank you."_

_With cries for more answers ringing out through the room, President Jacob Marshalls swiftly left the Press Room, and returned to his military escort._

_"Nicely presented, Mr. President."_

_"Thank you, Colonel. Now then, let's head back…"_

_It was then that a slow clap was heard, and the entire unit turned, guns drawn, to the direction where the clapping was heard._

_"A wonderful act, Mr. President."_

_"Who the fuck are you, and how did you get past my men?!"_

_"Calm yourself, Colonel. I am having a discussion with the President, please, don't be rude."_

_Marshalls stared coldly at this intruder._

_"You don't have a Press pass, how did you get in here?"_

_The intruder simply smirked._

_"You want to know what happened in Manhattan, correct?"_

_Marshalls frowned._

_"What do you know about that?"_

_"What do you know about Project BLACKWATCH?"_

_The colonel cringed at the name, while Marshalls just cocked an eyebrow._

_"What the Hell is BLACKWATCH?" He demanded, looking at the nervous colonel._

_"I-I'm sorry sir…I don't have the clearance to tell you…"_

_"Colonel Roberts, I am the President of the United States of America, your Commander-in-chief. Are you disobeying a direct order from your president?"_

_Roberts just shuddered, yet remained silent._

_"He is unable to answer, Mr. President, he answers to a higher authority than your public image portrays."_

_Marshalls glared at the intruder._

_"Now just who are you?"_

_The intruder smiled._

_"All in due time, Mr. President. Call a meeting of yourself and your cabinet. I shall be present, and I'll tell you what REALLY happened in Manhattan in 2009."_

_Roberts pointed his rifle at the intruder's face._

_"Are you giving the President orders?!"_

_"Stand down, Colonel." Marshalls ordered calmly._

_"Sir…!"_

_"I'll call for your meeting, Hell, I'll give you the clearance pass needed to get in, but I need a name."_

_The intruder turned and started walking away, but waved back as he shouted at Marshalls._

_"Rodney Schneidert! Director of Research at GENTEK!"_

* * *

**_Manhattan Island_**

**_52nd Street Cemetery_**

**_August 26th, 2011_**

One virus, three weeks, millions dead, because of me. As I walked through the cemetery, looking at the graves of thousands, I saw the dying faces of a thousand dead men and women, several of whom laid to rest here. Some so mangled they were unrecognizable, some just a grave without a body, as the body was consumed by me. This was when the reality of the monster I had become truly sank in, during situations like this.

"You may not be human, but from what I've been told, you are more human, more of a man, than Alex Mercer ever was."

As Ragland said this to me while we walked through the cemetery, my spirits lifted a bit. Mercer had done terrible things just to make his way in the world, and I cleaned up his biggest mistake. It still sat in my heart though, that his actions, my actions, caused the deaths of millions.

I crouched down beside a grave, for once not wearing the attire Blackwatch knew me in, just a dress shirt and nice outer wear, and looked at the gravestone.

Millions of people killed in three weeks. Millions killed by Mercer's self-importance and narcissism, including…

"Here lies Dana Alexandra Mercer

beloved journalist, friend, and sister.

1989-2009"

She never recovered from the coma, she just got worse. I never found out what Greene did to her, but I wish I had, I wish I'd gotten there sooner. Another death to pin on my head, Mercer's…My own, little sister.

Ragland just put a hand on my shoulder, like he did every year, and looked at me with his sympathy and sorrow as clear as day.

"I'm sorry Alex, I did everything I could, but this was not your fault."

"Alex Mercer…Whoever he was, his memories, his life, his sins…It's all inside me, all a part of me. Whoever Mercer was in life, I have to live with knowing it's part of my life now too."

Ragland just looked and smiled at me, I went through this broody tirade every year, this was nothing new to him.

Truth be told, if it weren't for Ragland, I don't think I ever would have picked myself back up after what nearly happened to New York. He was there to support me after the bomb, and after Dana, he was by far my one true friend. I was a wanted terrorist after the bomb went off, so I couldn't do anything legally in the U.S, let alone Manhattan, so Ragland let me stay with him. He provided food, shelter, and when I needed it, inconspicuous transportation.

I rubbed the stone one more time and got up, Ragland just looked at me and nodded.

"Ready to go?"

"Yeah."

We started walking off towards Ragland's car. As we got in I looked at him.

"I'm gonna be leaving Manhattan for a while."

Ragland just looked a bit shocked.

"Where will you go?"

"Fort Detrick."

"Maryland?! What the hell is out there?!"

"Blackwatch Command."

"Jesus Alex, things have just started cooling off, why go rile them up now?"

"There's still one more piece of the puzzle to find, Ragland."

"This is about Greene's child, isn't it?"

"You know what Greene did to Manhattan, now imagine that, on a global scale, tenfold. PARIAH is dangerous, and I'm probably the only one who can stop him. I have to do it before they unleash him."

Ragland just sat there and massaged his temples. He picked up that habit once I moved in, since I apparently had the power to, as he put it, 'verbally give him a headache, and eventually an ulcer.'

"I don't condone these actions Alex…"

"Even if he didn't go through this voluntarily, he is what he is now, Ragland."

"Let me finish. I don't condone your taking the actions, but I understand the necessity."

He looked at me with a pained smile as he started the car, and we drove off to his place.

Most of the ride was silent, just like most of our car rides. When we finally parked in front of his house, Ragland just looked at me.

"So, when're you heading out?"

"Probably about a month, let them think they're safe, get comfortable a little longer. Not too long though, the longer I wait, the more likely Blackwatch is to have made people who know what I need to know disappear. The truth behind Hope, behind Elizabeth Greene and her son, lies beneath the surface of Fort Detrick, and I need to find it before it gets erased forever."

Ragland just nodded at me and got out of the car. I shortly followed, went inside, shifted into my normal attire, and collapsed on his couch, as usual.

* * *

**_Maryland_**

**_Camp David_**

**_September 5th, 2011_**

**I sat down at the large table in what President Marshalls had made the meeting hall of Camp David. I had no idea why Director Schneidert called for my presence at this meeting of the most influential and powerful political figures in the United States. But, I figured he must have had his reasons.**

**President Marshalls started the meeting, standing at the head of the table and sternly looking over everyone in attendance.**

**"First off, thank you all for coming." He then looked at a television.**

**"Mr. Palmers, are the sound and visual clear?"**

**Secretary of Defense Palmers nodded.**

**"Yes, everything is set, Mr. President."**

**Even before 9-11, when an event such as this was held, where all the secretaries, the President and Vice-president gathered, at least one secretary would be absent, should god forbid something happen and the rest end up dead, so the chain of succession doesn't collapse.**

**"Good. Now then, I called this meeting under the advice of our guest, Dr. Rodney Schneidert, the Director of Research at GENTEK. The doctor apparently has information pertaining to the 2009 Manhattan incident. Doctor Schneidert, if you would."**

**With this, the President took his seat, and the Director stood, one of his calm and scheming smirks plastered on his face.**

**"Ladies and gentlemen, first I would like to thank you all for coming to this meeting. Now then, to business. Does anyone here know about Project BLACKWATCH?"**

**Not surprisingly, nobody said a word. I knew what he was doing, but as I was under orders to work for him, I stayed silent.**

**"Nobody? Okay. Well, let me begin by explaining exactly what BLACKWATCH was, and is."**

**President Marshalls crossed his arms over his chest and leaned back in his seat. I could tell he didn't like the Director, and I couldn't blame him. However, he knew Schneidert was the only lead he had to what really happened in Manhattan.**

**"BLACKWATCH was a program started back in the late '50s. It was the United States' first and only bio warfare unit. Their mission was to collect, test, and prepare any viruses or other biological material to be used against America's enemies. This led to project CARNIVAL, which used a virus referred to as Redlight. They tested it on chimpanzees and gathered amazing results, increased strength and intelligence being two key findings. After this, under the leadership of General Peter Randall, who was at that time a Colonel, they created Project CARNIVAL II, using military families as test subjects, gathering people from just about every ethnic background and placing them in Hope, Idaho. They were injected with the Redlight virus, being told that it was supposed to simulate fallout. For the next four years, nothing happened. Then, in 1969, the virus became active. It had started in children born in Hope, who quickly died. However, after these losses, the virus began to spread rapidly, infecting a large portion of the population. However, for at least half the year, Hope retained the façade of a perfectly safe and sterile environment. Things finally got out of hand, and the entire population became infected, all under the command of an 18 year old girl named Elizabeth Greene, codenamed MOTHER. The virus used Greene as a host, completely taking control of her body, as well as her mind. After experimentation, it was determined that the Redlight virus mutated within Greene, into what we now call the Blacklight virus.**

**Blackwatch responded with Operation ALTRUISTIC, in which the population of Hope was liquidated, save for Elizabeth Greene. After the Hope incident, BLACKWATCH's mission changed to the cataloguing, containment, and prevention of viral attacks on the United States. This led to the actual Blackwatch unit.**

**Over the next forty years, nothing happened, until Alex Mercer. Mercer was one of our Assistant Directors and worked directly under Director McMullen. GENTEK has worked very closely with Blackwatch since we started, we basically act as another branch of Blackwatch, and as such we have access to the Blacklight virus. Mercer was the lead geneticist on the Blacklight team, but he asked too many questions. The Blacklight project had too many leaks, and so General Randall began to liquidate it. One problem, Mercer caught on. In his eternal paranoid genius, he took a sample of the virus and ran. Blackwatch agents cornered him in Penn Station, where he released the virus as he was killed. From then on, we do not refer to the creature from the Manhattan incident as Alex Mercer."**

**I watched as President Marshalls cocked an eyebrow, I merely stayed silent and let the egomaniac talk some more.**

**"Blackwatch codenamed it as ZEUS."**

**This was when Marshalls finally had enough.**

**"Wait a moment Doctor. Are you telling me the United States military dehumanized this man?!"**

**I watched Director Schneidert twitch ever so slightly, and I smirked to myself. Not often I got to see him get pissed.**

**"Alex Mercer is no longer a man. It's not that the military dehumanized him, Mr. President. He dehumanized himself. Now please, sit down!"**

**I had to hold back my laughter as the President of the United States shot my current charge a glare that could kill, or at least imprison him for years, then begrudgingly sat down.**

**Finally Director Schneidert collected himself with a deep sigh and a flip of his hair.**

**"Thank you. Now then, Colonel, where was I?"**

**I sighed as I looked at him. I hated when he treated Blackwatch agents as his assistants, and even a simple question like this was layered with his sense of superiority.**

**"ZEUS, sir."**

**"Ah yes, thank you. Yes, Mercer has been re-dubbed with the codename ZEUS. All of the actions following Mercer's death and ZEUS' creation are recorded in these files. Here, Mr. President."**

**Schneidert then handed him the files and continued.**

**"Most of those files are from Director McMullen's personal journals. Following his death, they were filled with the official Blackwatch reports which were supposed to have been burned after reviewed. I personally saw to the prevention of this."**

**There he went again, layering on how he prevented something horrible from occurring, just showing us all how important he really is.**

**"Some areas are a little fuzzy, but I have my own theories about what happened. What matters now is that ZEUS is still alive and active. With your clearance, Mr. President, I would like to start a above top secret clearance project."**

**This was a surprise to me. Normally for Director Schneidert to begin projects, top secret or otherwise, he had to go through Blackwatch Command first. This was definitely NOT going by the book.**

**"What kind of project is this?"**

**"ZEUS was created through the death of Alex Mercer. Something about the circumstances of Mercer's death led to ZEUS, and ZEUS is unlike anything that GENTEK or Blackwatch has ever seen before. The virus has mutated into something beyond our understanding. For all intents and purposes, the Blacklight Virus has created the Ultimate Shapeshifter, something that with our current technology standards we have no hope of defeating. I propose we recreate the scenario that created ZEUS. Use a team of several different personnel, volunteers of course, and create a unit capable of fighting ZEUS on its own terms. Colonel Finnigan, please stand."**

**I blinked a few times as I stood.**

**"Mr. President, this is Colonel Adam Joshua Finnigan, a top-notch Blackwatch Agent, he has served on several Runner hunts with the late Captain Robert Cross, and…"**

**"Thank you, Doctor Schneidert. I believe that Colonel Finnigan can speak for himself, can he not?"**

**I nearly broke out laughing at the look on Schneidert's face when he realized he'd basically been told to shut up. I wish I'd said it, still do, the bastard was ALWAYS talking!**

**"Now then, Colonel, I assume that your presence here means you would volunteer for this program?"**

**At this point I was already resisting the urge to throw Schneidert through a wall. I had figured out he set me up, and he knew I would never say no to the President. Along with this, he had read my file, and knew that I lost several friends to Mercer in Manhattan.**

**However…**

**"Sir…"**

**I'd play along for now.**

**"…Absolutely."**

**At this, I saw a hint of sadness and concern in the President's face as he addressed me.**

**"You do realize that if your death is the same as Mercer's, you will likely suffer his memory loss symptoms explained in these reports?"**

**"Yes, sir."**

**"What about your family, son?"**

**"The Union is my family, sir, and I would die defending it. Such is the oath of a Blackwatch soldier."**

**I watched Marshalls sigh and rub his head, then look at Schneidert.**

**"Very well, Doctor Schneidert. You can have your program. What did you wish to call it for the records?"**

**Schneidert just smiled.**

**"SHADOWSTEP, for Shapeshifters walk in the shadows of deceit, as will this team of Shapeshifters."**

**

* * *

**

**A/N: Well? How was it? I know that Schneidert didn't mention PARIAH, and there is a reason for that, which he will explain next chapter. I hope the perspective jumps didn't confuse anyone, I will be using them for the entire story. If anyone has any questions or concerns, please either PM me or leave them in reviews. Now then, if you'll excuse me, Uchiha Avenger is waiting! Next chapter of it should be up some time next week, permitting that things don't escalate between me and my old man…**

**BlackChaos, out.**


End file.
